Contacts of the helix formed by residues 890 - 894 (chain A) in PDB entry 5IYB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 890 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877A ALA* 3.6 14.1 - - + +
879A VAL* 4.8 0.7 - - - -
888A GLN* 3.5 11.2 - - - +
889A LEU* 1.3 87.8 + - + +
891A TYR* 1.3 66.1 + - - +
892A GLY 3.2 1.2 + - - -
893A GLU* 3.1 15.9 + - - -
894A ASP* 4.3 4.5 - - - +
895A GLY* 3.8 18.4 - - - +
1022A ILE* 3.5 27.7 - - - +
1023A VAL* 3.1 47.1 + - + +
1024A ASN 4.6 1.6 + - - -
1030A SER* 4.4 5.9 + - - +
1033A ALA* 3.6 38.3 + - - +
1034A GLN* 2.9 28.7 + - - +
1037A ALA* 3.9 7.0 - - - +
163E TYR* 5.1 8.3 + - - -
203E TYR* 4.8 3.6 - - + -
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Residues in contact with TYR 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873A VAL* 4.6 6.5 - - + -
877A ALA* 3.9 6.5 + - - +
879A VAL* 3.7 25.1 - - + -
888A GLN* 4.2 3.8 - - - -
890A ARG* 1.3 69.6 - - - +
892A GLY* 1.3 61.1 - - - +
894A ASP* 2.6 26.2 - - - +
895A GLY* 3.3 9.9 + - - +
896A LEU 3.8 18.7 + - - +
897A ALA* 4.5 8.5 - - - -
898A GLY 4.7 3.4 + - - -
1081A ALA* 4.0 23.3 - - + -
1087A VAL* 3.5 45.7 + - + +
1090A LEU* 4.9 4.1 - - + +
1091A ALA* 5.2 0.5 - - - +
1396A ARG* 4.3 19.0 - - + +
1397A HIS* 3.8 26.7 + - - -
1400A LEU* 4.4 16.8 - - + -
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Residues in contact with GLY 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888A GLN* 2.8 23.6 + - - -
890A ARG 3.2 0.2 + - - -
891A TYR* 1.3 78.9 - - - +
893A GLU* 1.3 69.9 + - - +
894A ASP* 3.3 9.2 - - - +
1395A TYR* 4.8 5.5 - - - -
1396A ARG* 4.3 28.4 - - - +
1399A ALA* 5.3 1.6 - - - -
199E THR* 3.7 9.5 + - - -
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Residues in contact with GLU 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888A GLN* 4.0 12.0 + - - +
890A ARG* 3.1 12.2 + - - -
892A GLY* 1.3 78.2 - - - +
894A ASP* 1.3 63.4 + - - +
1037A ALA* 5.2 2.1 - - - +
1375A ARG* 3.0 28.4 + - - -
1395A TYR* 3.6 19.9 + - - -
1399A ALA* 4.9 0.9 - - + -
195E ARG* 3.3 8.1 + - - -
196E PRO 5.2 0.8 - - - +
197E SER* 3.2 24.7 + - - +
199E THR* 4.1 0.6 + - - +
200E ALA* 3.1 19.9 - - - +
203E TYR* 3.1 58.0 - - + +
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Residues in contact with ASP 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890A ARG* 4.1 6.2 + - - +
891A TYR 2.6 28.6 - - - +
892A GLY 3.3 8.6 - - - +
893A GLU* 1.3 77.4 - - - +
895A GLY* 1.3 59.9 + - - +
896A LEU* 3.2 29.1 + - + +
1022A ILE* 3.5 21.6 - - - +
1037A ALA* 4.3 13.8 - - - +
1038A THR* 5.6 0.2 - - - +
1396A ARG* 2.8 38.5 + - - -
199E THR* 3.7 16.5 - - - +
200E ALA* 4.3 7.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il